Your preferred intonation method.

Maybe you should try this on your turbo and quantify the actual differences for us.
You can only see if it is out. I doesn't quantify it because it only has a single strobe line. I trust the turbo because it sounds " in"to my ears and I rarely think that about any tuner. I can only compare it to other tuners and have no additional way to calibrate it. If you like using the capo and it works for you then go for it but I still wouldn't recommend it.
 
1/1000th of a semitone is darn accurate. My Peterson Stroboflip does a great job. But I haven’t had to use it on my last two new guitars that came from Sweetwater and were perfect. Also the one was a Standberg which played extremely well and only my core PRS’s were equal in precision. There’s a few things to know about the Strandberg bridge system especially the tremolo when doing a setup. It takes some patience the first time through.

One thing I would hope everyone knows, and that’s a change from one brand of string to another and especially one gauge to another will definitely need intonation performed and preferably the nut gone over.
Yes change anything and you will need to at least check it. The worst is calibrated strings on a Steinberger TT intonate and then calibrate the trem. Sometimes the high E is out in length and won't calibrate. 1/10th of a cent is 1/1000th of a tone and you can hear the difference when you tune with a Turbo, it sounds better to me but I have no way to test how accurate it is.
 
You can only see if it is out. I doesn't quantify it because it only has a single strobe line. I trust the turbo because it sounds " in"to my ears and I rarely think that about any tuner. I can only compare it to other tuners and have no additional way to calibrate it. If you like using the capo and it works for you then go for it but I still wouldn't recommend it.
Wait, what Turbo tuner are you talking about that has 1/50th of a cent accuracy? If it's the AxeFX, doesn't it literally display how many cents it is off?

Also, you mentioned "why do things that even theoretically create anomaly," which is interesting. What is the theory that says that the difference in degree of breakover angle between a string that is barely fretted versus one that is driven down to the wood will contribute to a change in how that string is going to intonate?
 
Wait, what Turbo tuner are you talking about that has 1/50th of a cent accuracy? If it's the AxeFX, doesn't it literally display how many cents it is off?

Also, you mentioned "why do things that even theoretically create anomaly," which is interesting. What is the theory that says that the difference in degree of breakover angle between a string that is barely fretted versus one that is driven down to the wood will contribute to a change in how that string is going to intonate?
The contact point on the fret is different slightly if you press too hard and it has a cumulative effect also you are playing the guitar with you hand so fret it the same way. The Turbo Tuner by sonic research is the only tuner that can do a 1/50th of a cent.
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Best tuner you can buy.
 
I have that tuner! I'm restringing an axe now and I'll try my experiment with the ST-300 and see if I can see a difference with those same two capos I tried before.

PS - I didn't realize that was more accurate than my Peterson. Surprising!
 
I have that tuner! I'm restringing an axe now and I'll try my experiment with the ST-300 and see if I can see a difference with those same two capos I tried before.

PS - I didn't realize that was more accurate than my Peterson. Surprising!
It will be interesting, If you bend down the string toward the fingerboard it contacts the fret nearer the capon perfectly on the top. This effect will also be more noticeable on worn frets with a wider contact point ( this could be why you'r not seeing anything) and projects the string up at a slight angle.
 
Also if you have a perfectly crowned fret the capo may make such a small difference as to not show but use it on something with fret wear or just a wide flat top on the fret the results will be more noticeable .
 
OK, a couple of things to report:

First, I would also generally suggest that you try to use your neck pickup and turn the tone control down all the way when doing intonation. What I was taught is that this helps to eliminate some of the higher harmonics that the tuner can see, and which might throw it off a little.

The Turbo tuner did great, and was indeed registering some changes that the Peterson had not. Or else it was just easier to read. I'd forgotten I even had that tuner, tucked away in a guitar case pocket.

However, the difference made by the two different capos (one really soft, one really pressing hard) was much less than even the changes I could make just by rotating my fretting finger ever so slightly.

So from the sample size of 1 (take it with a shaker of salt), on this guitar with these strings, the difference between capos seems to be down in the noise of all the other variables.
 
Related: If you suddenly experience unusual intonation issues on a particular string, it may be the string. I had a bad string send me down a WTF rabbit hole until it dawned on me to replace it, and it was all back to normal intonation. (Must of been some weird non-linear distribution of mass on that string to cause an issue like that.)
 
After switching from the Babicz bridge back to my stock Fender I did 3 things Andy suggested. I pushed down on the strings to seat them at the crown of the saddle, I reduced my neck relief to near flat and what impacted my setup the most was the 3rd/15th method to set intonation. Gotta' say I'm pretty impressed with this method.
 
If the guitar is in tune and I press very lightly on the first fret it's ok but if I press any harder a few strings go very sharp. Does this mean the nut maybe to high on these strings?
 
If the guitar is in tune and I press very lightly on the first fret it's ok but if I press any harder a few strings go very sharp. Does this mean the nut maybe to high on these strings?
Probably, but if it sounds in tune while you're playing it's fine. Do you like the way it plays/feels?
 
OK, a couple of things to report:

First, I would also generally suggest that you try to use your neck pickup and turn the tone control down all the way when doing intonation. What I was taught is that this helps to eliminate some of the higher harmonics that the tuner can see, and which might throw it off a little.

The Turbo tuner did great, and was indeed registering some changes that the Peterson had not. Or else it was just easier to read. I'd forgotten I even had that tuner, tucked away in a guitar case pocket.

However, the difference made by the two different capos (one really soft, one really pressing hard) was much less than even the changes I could make just by rotating my fretting finger ever so slightly.

So from the sample size of 1 (take it with a shaker of salt), on this guitar with these strings, the difference between capos seems to be down in the noise of all the other variables.
Well the whole thing was worth it to rediscover your turbo tuner and satisfy yourself that on this particular guitar the use of a capo when intonating is not problematic. I still have to recommend using your fretting hand to others though because it helps to standardise a process across guitars that may not have perfectly crowned or worn frets. But in your case it certainly is not going to make much difference although you did see something at the extreme end.
 
Another guide is if your intonation pattern is anything different from the common expected one then something is wrong. Either a poor contact with the saddles or the string is bad.
You should ALWAYS get a slight variation of this;
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Only changing according to the gauge of string.
 
This is not true that they have an issue BUT a brand new string in a thicker gauge when forced over a saddle at a sharp angle ( as in a Fender Strat) will continue to arc forward until it beds down and the core bends. While this is happening the intonation point is actually in front of the witness point hence you can't seem to put the saddle far enough back. The solution is simply press down on the string just in front of the saddle to ensure a proper contact with the witness point. Suddenly you need to intonate the guitar again and it is within the saddle range.
I’ve been doing this for years, I just remember one day seeing the string go over the saddle in a slight arc and thought “that’s not right” and pressed it down so that it proper straight. Just thought it was something to help along with string stretching, never thought about how it would help intonation as well 🤔
 
I’ve been doing this for years, I just remember one day seeing the string go over the saddle in a slight arc and thought “that’s not right” and pressed it down so that it proper straight. Just thought it was something to help along with string stretching, never thought about how it would help intonation as well 🤔
This is the biggest cause of false intonation readings during set up . A big issue with acoustics too. If you don't press the strings down on thicker wound sizes most acoustics play out of tune until you do or they bed down themselves.
 
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